Put the beans in a large saucepan and pour in enough cold water to cover them by at least 2 inches.
Bring to a boil, let boil for 2 minutes, then let the beans soak in the water off the heat for about 1 hour.
Bring them to a boil again, add 1 onion and 1 teaspoon of the salt, half cover the pan and simmer the beans as slowly as possible for about 30 minutes, or until they are partially done.
Drain the beans and discard the onion and bean water.
Preheat the oven to 250°.
To bake the beans, choose a traditional 2 1/2-quart bean pot or a heavy casserole with a tight-fitting cover.
Place 2 onions, each stuck with 2 cloves, in the bottom of the bean pot or casserole and cover with the beans.
In a small mixing bowl, combine the molasses, 3/4 cup of the brown sugar, mustard, and 1 teaspoon each of salt and black pepper.
Slowly stirring with a large spoon, pour in the 2 cups of water.
Pour this mixture over the beans and push the salt pork slightly beneath the surface.
Cover tightly and bake in the center of the oven for 4 1/2 to 5 hours.
Then remove the cover and sprinkle with the remaining 1/4 cup of brown sugar.
Bake the beans uncovered for another 1/2 hour.